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LOC129391005 MPRA-validated peak3184 silencer [ Homo sapiens (human) ]

Gene ID: 129391005, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129391005
Gene description
MPRA-validated peak3184 silencer
Gene type
biological region
Feature type(s)
regulatory: silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region was identified as an uncharacterized cis-regulatory element (CRE) that lacked a promoter, enhancer or CTCF-bound insulator chromatin signature. It was validated as a silencer that could repress activity of a super core promoter (SCP1) by STARR-seq massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells. [provided by RefSeq, Apr 2023]
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Genomic context

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See LOC129391005 in Genome Data Viewer
Location:
chromosome: 18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (74300481..74300681)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (74528031..74528231)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (71967716..71967916)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 551, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:71904867-71905366 Neighboring gene Sharpr-MPRA regulatory region 12176 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr18:71917515-71918450 Neighboring gene cytochrome b5 type A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:71935092-71935632 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50263 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50279 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:71948314-71948841 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50293 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:71957777-71958384 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50303 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50301 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13495 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50307 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50330 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50334 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50341 Neighboring gene chromosome 18 open reading frame 63 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50347 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_50353 and experimental_50354 Neighboring gene NANOG hESC enhancer GRCh37_chr18:72050693-72051551 Neighboring gene FAU pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Candidate silencer elements for the human and mouse genomes. Doni Jayavelu N, et al. Nat Commun, 2020 Feb 26. PMID 32103011, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_156635.1 

    Range
    101..301
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    74300481..74300681
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    74528031..74528231
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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